Most human tumors, particularly those derived from epithelial cancers, exhibit global genomic alterations that make it difficult to identify mutations critical for cell transformation and to define the consequences of specific cancer-associated mutations. Recent advances in sequencing technologies and comprehensive methods to map cancer-associated amplicons and deletions now make it possible to identify all of the genetic alterations harbored by a particular tumor, and large-scale efforts such as TCGA to apply these technologies have already begun to provide comprehensive views of cancer genomes. Despite these important advances, a critical bottleneck in translating these discoveries into therapies that will enter the clinic remains the functional characterization of genes as potential therapeutic targets (genetic elements of interest, GEOI). Specifically, although the identification of genes that are mutated in a substantial fraction of particular cancer types is an essential first step, the parallel development of efficient methods to annotate the function of cancer-associated genes is necessary to distill promising candidate cancer targets from this structural description of cancer genomes. Thus, functional annotation of cancer genes will identify those genes whose protein products are essential for tumor initiation or maintenance and will provide critical insights into the biochemical pathways that are dysregulated in these same cancers. This information will accelerate the development of new molecularly targeted therapeutics. We have recently developed the methods and tools necessary to take an integrated approach that combines the high throughput functional characterization of cancer genomes with the emerging knowledge from on-going genome characterization efforts. In this application, we propose an integrated pipeline that (1) will combine a whole genome loss-of-function and gain- of-function approaches to uncover candidate cancer gene function with the information derived by TCGA on genetic alterations found in brain (GBM) and ovarian (OVCA) cancer and (2) will provide this information and reagents to the cancer research community without restrictions. The information obtained by these studies will facilitate investigator-initiated basic and translational studies and accelerate the development of new therapeutic approaches. Given the poor prognosis associated with these diseases, we anticipate that impact of this program will be both major and timely. Moreover, this program can be executed within 2 years and will require additional personnel to complete. As such, this program is consistent with the goals of the NIH Challenge Grant Program and the American Recovery and Reinvestment Act of 2009. Although focused on GBM and OVCA, this project will provide a foundation for the broad functional annotation of cancer genomes.